Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015014.1 Corchorus olitorius cultivar O-4 contig15047, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 14425
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.34
Found at i:128 original size:39 final size:39
Alignment explanation
Indices: 48--130 Score: 98
Period size: 39 Copynumber: 2.1 Consensus size: 39
38 CCACGCAGCA
* *
48 GGCCCGCGCGCCTAGCCTGGCGCGCTTGGGCCGTGCGCT
1 GGCCCGCGCGCCTAGCCTGGCACGCTTGGGCCATGCGCT
* *
87 GGCCCGCGCGCCT-GGCTTGCACG-TTGGGCCATGCTGACT
1 GGCCCGCGCGCCTAGCCTGGCACGCTTGGGCCATGC-G-CT
126 GGCCC
1 GGCCC
131 ATTGGCCTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
37 10 0.26
38 8 0.21
39 20 0.53
ACGTcount: A:0.05, C:0.40, G:0.39, T:0.17
Consensus pattern (39 bp):
GGCCCGCGCGCCTAGCCTGGCACGCTTGGGCCATGCGCT
Found at i:2082 original size:20 final size:20
Alignment explanation
Indices: 2057--2094 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2047 GATTAAAAGT
2057 TGATAAAGTTACTAAAATCA
1 TGATAAAGTTACTAAAATCA
*
2077 TGATAAATTTACTAAAAT
1 TGATAAAGTTACTAAAAT
2095 TAGTAAGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.08, G:0.08, T:0.34
Consensus pattern (20 bp):
TGATAAAGTTACTAAAATCA
Found at i:7312 original size:12 final size:12
Alignment explanation
Indices: 7292--7321 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
7282 AACAACAGAA
7292 GCAACAAGATCAG
1 GCAA-AAGATCAG
7305 GCAAAAGATCAG
1 GCAAAAGATCAG
7317 GCAAA
1 GCAAA
7322 TGCTTGTTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 13 0.76
13 4 0.24
ACGTcount: A:0.50, C:0.20, G:0.23, T:0.07
Consensus pattern (12 bp):
GCAAAAGATCAG
Found at i:12164 original size:6 final size:6
Alignment explanation
Indices: 12155--12202 Score: 69
Period size: 6 Copynumber: 7.8 Consensus size: 6
12145 ATAATATTAA
* *
12155 TATATC TATATC TATATC TATATC TATATA TATATT TATATAC TATAT
1 TATATC TATATC TATATC TATATC TATATC TATATC TATAT-C TATAT
12203 AAGTCTAAAC
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
6 33 0.87
7 5 0.13
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.52
Consensus pattern (6 bp):
TATATC
Found at i:12516 original size:116 final size:114
Alignment explanation
Indices: 12309--12631 Score: 476
Period size: 114 Copynumber: 2.8 Consensus size: 114
12299 TCCAACCGAA
* * *
12309 TTTTATTTCCATATTAAGAAAGTC-T-AA-AATAATAACAATTATTTTTACATTAAACAACTTAT
1 TTTTCTTTCCATATTAA-AAAGTCTTAAATAATACTAACAATT-TTTTTACGTTAAACAACTTAT
* *
12371 TATTATAATTATTAAAATTATTATTAGTTATATATATCATTGGTCATTAAGT
64 TATTATAATTATTAAAATTATTATTAGTTATATATATCATTAGTCATT-ACT
12423 TTTTCTTTCCATATTATAAAAGTCTTAAATAATACTAACAATTTTTTTACGTTAAACAACTTATT
1 TTTTCTTTCCATATTA-AAAAGTCTTAAATAATACTAACAATTTTTTTACGTTAAACAACTTATT
12488 ATTATAATTATTAAAATTATTATTAGTTATATATATCATTAGTCATTACT
65 ATTATAATTATTAAAATTATTATTAGTTATATATATCATTAGTCATTACT
* * * *
12538 TTTTCTTTCCATATTAAAAAATTTTAAAATAATACTAACAA-TTTTTTACGTTAAACATCTTCTT
1 TTTTCTTTCCATATTAAAAAGTCTT-AAATAATACTAACAATTTTTTTACGTTAAACAACTTATT
*
12602 ATTATAATTATTAAACTTATTATTA-TTATA
65 ATTATAATTATTAAAATTATTATTAGTTATA
12632 ACAATTATTA
Statistics
Matches: 194, Mismatches: 10, Indels: 11
0.90 0.05 0.05
Matches are distributed among these distances:
113 5 0.03
114 73 0.38
115 35 0.18
116 69 0.36
117 12 0.06
ACGTcount: A:0.40, C:0.10, G:0.03, T:0.47
Consensus pattern (114 bp):
TTTTCTTTCCATATTAAAAAGTCTTAAATAATACTAACAATTTTTTTACGTTAAACAACTTATTA
TTATAATTATTAAAATTATTATTAGTTATATATATCATTAGTCATTACT
Found at i:12626 original size:15 final size:16
Alignment explanation
Indices: 12603--12650 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 16
12593 CATCTTCTTA
*
12603 TTATAATTATTA-AAC
1 TTATTATTATTATAAC
12618 TTATTATTATTATAAC
1 TTATTATTATTATAAC
12634 AATTATTATTAGTTATA
1 --TTATTATTA-TTATA
12651 TGATCACTAC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 11 0.39
16 3 0.11
18 9 0.32
19 5 0.18
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (16 bp):
TTATTATTATTATAAC
Found at i:12639 original size:18 final size:17
Alignment explanation
Indices: 12600--12650 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 17
12590 AAACATCTTC
* *
12600 TTATTATAATTATTAAAC
1 TTATTATTATTA-TAAAA
12618 TTATTATTATTATAACAA
1 TTATTATTATTATAA-AA
12636 TTATTATTAGTTATA
1 TTATTATTA-TTATA
12651 TGATCACTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 3 0.10
18 21 0.72
19 5 0.17
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.53
Consensus pattern (17 bp):
TTATTATTATTATAAAA
Found at i:14058 original size:22 final size:22
Alignment explanation
Indices: 14028--14069 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
14018 GAGATAATAA
* *
14028 TATAGTTTTTAGAATAATCACT
1 TATACTTTTTAGAACAATCACT
14050 TATACTTTTTAGAACAATCA
1 TATACTTTTTAGAACAATCA
14070 TTGAAACTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.43
Consensus pattern (22 bp):
TATACTTTTTAGAACAATCACT
Found at i:14081 original size:23 final size:22
Alignment explanation
Indices: 14033--14081 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
14023 AATAATATAG
* *
14033 TTTTTAGAATAATCACTTATAC
1 TTTTTAGAACAATCACTTAAAC
14055 TTTTTAGAACAATCA-TTGAAAC
1 TTTTTAGAACAATCACTT-AAAC
14077 TTTTT
1 TTTTT
14082 TAGTAACTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 2 0.08
22 22 0.92
ACGTcount: A:0.35, C:0.12, G:0.06, T:0.47
Consensus pattern (22 bp):
TTTTTAGAACAATCACTTAAAC
Done.